At present, a major challenge of genomic and genetic studies in livestock species is the identification and mapping of individual quantitative trait loci (QTL) and quantitative trait genes (QTG) that control agricultural traits. Candidate genes are typically chosen based on the results of previous linkage mapping studies and on comparative biological or physiological functions in other species (Rothschild and Soller, 1997). A review of recent publications shows that many QTL have been mapped for traits of economical importance in dairy cattle (see e.g. Khatkar et al., 2004). However, despite the large number of QTL studies in cattle and other species, little progress has been made on the identification of major genes affecting milk production, fertility and health traits in dairy cattle. One major limitation when choosing a candidate gene is the large number of provisional genes present in most QTL regions.
Reproductive performance in high-producing dairy cows is currently suboptimal and continues to decline as characterized by low fertilization rates and reduced embryonic survival (Moore and Thatcher, 2006). The decrease in fertility in dairy cattle is a worldwide problem. In the U.S.A., the first-service conception rate has been decreasing for many years with an estimated decline of 0.45% per year over a 20-year period (Butler and Smith, 1989). Lucy (2001) estimated that the first-service conception rate had declined from about 65% in 1951 to 40% in 1996. In the U.K., the conception rate is declining at about 1% per year, and at first-service it is currently lower than 40% (Royal et al., 2000). The reasons for the reduced reproductive efficiency are manifold, but it seems likely that there are substantial genetic effects contributing to this infertility, despite the low heritability of most fertility traits (VeerKamp and Beerda, 2007). Shook (2006) estimated that genetics account for about one-third of the decrease in daughter pregnancy rates.
Despite the large number of quantitative trait loci studies in cattle and other species, little progress has been made on the identification of major genes affecting reproduction traits (Veerkamp and Beerda, 2007). The present inventors previously have identified single nucleotide polymorphisms (SNPs) that may be used to predict improved fertility in dairy cattle, including those located in the signal transducer and activator 5A (STATA), known to play an important role in cytokine signaling pathways. See e.g. Khatib et al., 2008.
Such major genes would facilitate genetic testing of bulls that enable quick and accurate evaluation of its fertility and the survival rate of embryos conceived from these bulls. Genetic testing of the bulls to determine their fertility and embryo survival rate can lower the high cost of the traditional, progeny testing methods, by by-passing the need to produce live birth.
In addition, identification of major genes that affect reproduction traits can facilitate marker-assisted selection, which can lower the high cost of progeny testing currently used to improve sires. With marker-assisted selection, young bull progeny could be evaluated immediately after birth or even before birth, and those young bulls that are determined by genetic testing to have undesirable markers would never be progeny tested, for the presence/absence of the marker.
The present disclosure provides such a genetic marker that can be used for genetic testing and for marker-assisted selection process.